Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis      
dateReleased:
08-07-2012
description:
The relationship between epigenetic marks on chromatin and the regulation of DNA replication is poorly understood. Mutation of the H3K27 methyltransferase genes, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, result in re-replication (repeated origin firing within the same cell cycle). Here we show that mutations that reduce DNA methylation act to suppress the re-replication phenotype of atxr5 atxr6 mutants. This suggests that DNA methylation, a mark enriched at the same heterochromatic regions that re-replicate in atxr5/6 mutants, is required for aberrant re-replication. In contrast, RNA sequencing analyses suggest that ATXR5/6 and DNA methylation cooperatively transcriptionally silence transposable elements (TEs). Hence our results suggest a complex relationship between ATXR5/6 and DNA methylation in the regulation of DNA replication and transcription of TEs. DNA-seq: One gram of mature rosette leaves were collected from 3-4-week-old plants, chopped in 0.5 ml of filtered Galbraith buffer, and stained with propidium iodide. A BD FACS Aria II in the UCLA Jonsson Comprehensive Cancer Center (JCCC) Flow Cytometry Core Facility was used to sort the nuclei. For sequencing, 7,000-9,000 8C nuclei of each sample were collected, and purified DNA with Picopure purification kit (Arcturus) following manufacturer instructions. RNA-seq: RNA-seq experiments were performed in two biological replicates for each genotype. 0.1g of tissue was ground in Trizol. Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina). BS-seq: 0.5-1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-38286
refinement:
raw
alternateIdentifiers:
38286
keywords:
functional genomics
dateModified:
02-29-2016
availability:
available
types:
gene expression
name:
Arabidopsis thaliana
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-38286/E-GEOD-38286.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-38286/E-GEOD-38286.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38286
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.